I suppose this is an issue with FreeCAD, since Z88 can already handle multiple beam sections. So you basically have two options:
1. Use only Z88Aurora (or Z88OS) in your workflow. You can create truss structures entirely in Z88Aurora.
2. You can update the FreeCAD module to support multiple beam sections. I looked into the code, it's located in /src/Mod/Fem/FemInputWriterZ88.py